Copyright © 2001, Institut national de la
santé et de la recherche médicale
(INSERM)
NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.
Bookshelf ID: NBK7107PMID: 21413366
Mapping Protein/DNA Interactions by Cross-Linking
Presents the process of mapping the genetic interactions of protein and DNA via cross-linking.
Contents
- Dissecting Fission Yeast Centromeres via SilencingRobin Allshire.
- Localizing Replication Sites and Nuclear ProteinsAngela Taddei, Danièle Roche, Jean-Baptiste Sibarita, Sébastien Huart, Christèle Maison, Delphine Bailly, and Geneviève Almouzni.
- Finding Downstream Target DNAs for Chromatin Proteins by X-CHIP in DrosophilaNicolas Nègre and Giacomo Cavalli.
- Emerging Techniques: UV Laser Footprinting and Protein--DNA CrosslinkingStefan Dimitrov.
- Nuclear Organization and Gene Expression: Visualization of Transcription and Higher Order Chromatin StructureRoel van Driel and Pernette J Verschure.
- Examining the Distribution of Telomeric and DNA Repair Proteins by ChrIP and Real-Time PCRKarine Dubrana.
- Nuclear Organisation and Gene Silencing in LymphocytesAmanda Fisher and Matthias Merkenschlager.
- Direct Visualization of Transcription Factor Binding to Regulatory Elements in Living CellsGordon L Hager.
- Part I. Chromatin Protein Complexes: Dynamic Assemblies in the NucleusDonna Jovin.
- Isolation of Homeodomain Engrailed Target Genes by UV Cross-Linking and Chromatin IPFlorence Maschat.
- Analysis of Chromatin Assembly, Chromatin Domains, and DNA Replication Using Xenopus SystemsJean-Marc Lemaitre, Yegor Vassetzky, and Marcel Méchali.
- Collection of Eggs
- Low-Speed Egg Extract (LSE)
- Preparation of High-Speed Extract (HSE)
- Preparation of Demembranated Sperm Nuclei
- Assays for DNA Replication in Xenopus Extracts
- DNA Replication Assay by TCA Precipitation
- Calculation of the Activity of the Extract
- Detection of Protein Interaction with Chromatin by Immunolocalisation
- Detection of Protein Interaction with Chromatin by a Purification Assay
- Protocol for Single-stranded DNA Replication and Chromatin Assembly
- Notes
- Chromatin Assembly
- Supercoiling Assay (First Method)
- Supercoiling Assay (Second Method)
- Micrococcal Nuclease Digestion Assay
- Notes
- Studying DNA--Protein Interactions in Vivo Using LM-PCR Coupled with Nuclear Matrix Isolation
- Protocol for the Nuclear Matrix Isolation
- Ligation-mediated PCR
- Appendix: Buffers and Solutions
- References
- Binding Sights in Chromatin by X-ChIPAchim Breiling and Valerio Orlando.
- Chromatin Immunoprecipitation in Budding YeastTomoyuki Tanaka.
- ChIP with Native Chromatin: Advantages and Problems Relative to Methods Using Cross-Linked MaterialBryan Turner.
- Highly Sensitive FISH in Combination with the Visualization of the Mammalian Genome: ArchitectureDaniele Zink.
- Part II. Fly-FISHing: A Protocol to Localize Single Copy Genes inside the Nucleus in Whole Mount EmbryosMark J Gemkow.
- Part 2. Detailed Method for Immunoprecipitation of Unfixed Chromatin from Mammalian CellsLaura O'Neill and Bryan Turner.
- Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation.[Biotechniques. 2005]Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation.Nowak DETian B, Brasier AR, . Biotechniques. 2005 Nov; 39(5):715-25.
- Mapping protein-protein interactions between MutL and MutH by cross-linking.[J Biol Chem. 2004]Mapping protein-protein interactions between MutL and MutH by cross-linking.Giron-Monzon LManelyte L, Ahrends R, Kirsch D, Spengler B, Friedhoff P, . J Biol Chem. 2004 Nov 19; 279(47):49338-45. Epub 2004 Sep 14.
- Cross-linking of DNA-binding proteins to DNA with psoralen and psoralen furan-side monoadducts. Comparison of action spectra with DNA-DNA cross-linking.[J Biol Chem. 1997]Cross-linking of DNA-binding proteins to DNA with psoralen and psoralen furan-side monoadducts. Comparison of action spectra with DNA-DNA cross-linking.Sastry SSRoss BM, P'arraga A, . J Biol Chem. 1997 Feb 7; 272(6):3715-23.
- Review Identification and mapping of protein-protein interactions by a combination of cross-linking, cleavage, and proteomics.[Bioconjug Chem. 2005]Review Identification and mapping of protein-protein interactions by a combination of cross-linking, cleavage, and proteomics.Trakselis MAAlley SC, Ishmael FT, . Bioconjug Chem. 2005 Jul-Aug; 16(4):741-50.
- Review A new cross-linking strategy: protein interaction reporter (PIR) technology for protein-protein interaction studies.[Mol Biosyst. 2010]Review A new cross-linking strategy: protein interaction reporter (PIR) technology for protein-protein interaction studies.Tang XBruce JE, . Mol Biosyst. 2010 Jun; 6(6):939-47. Epub 2010 Mar 16.
- Mapping Protein/DNA Interactions by Cross-LinkingMapping Protein/DNA Interactions by Cross-LinkingBookself
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